|
| Status |
Public on Dec 22, 2010 |
| Title |
control cells rep2 |
| Sample type |
RNA |
| |
|
| Source name |
RO82 W_1 control-rep2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RO82-W-1
disease state: carcinoma
treatment: none
|
| Treatment protocol |
RO82 W-1 cells were treated five hours a day for four days with the calcium ionophore ionomycin made up to a final concentration of 2 µM in the PSS medium containing 2mM calcium, that may increased intracellular calcium up to 2 nM. We further used the cytosolic calcium chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl ester (BAPTA/AM) made up to a final concentration of 2-8 µM, with a combination of ionomycin and BAPTA/AM or with equivalent volumes of DMSO for control cells. To avoid cell death due to the toxic effects of intracellular Ca++ ion chelation, the BAPTA/AM concentration was adjusted to cell density in the flask for each day of treatment as follows: 2 µM the first day, 4 µM the second day, 6 µM the third day, and 8 µM the fourth day
|
| Growth protocol |
RO82 W-1 cells were grown in a mixed 60:30 DMEM-F12/endothelial basal medium supplemented with 10% fetal bovine serum, 1% L-glutamine, and an antibiotic cocktail
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using the RNeasy kit . The integrity of RNA was determined using a Bio-Analyzer 2100
|
| Label |
Cy3
|
| Label protocol |
RNA amplification and cDNA labeling using Cy3/Cy5 dyes according to manufacturer’s recommendations (Agilent)
|
| |
|
| Hybridization protocol |
Agilent hybridization protocol was used
|
| Scan protocol |
Agilent scanner
|
| Description |
Biological replicate 2 of 2. Control cells, untreated
|
| Data processing |
Data tables contain Genespring software computed values. We have selected data after filtering normalized data on non variation for gene expression through all the chemical conditions (ionomycin and BAPTA treatment compared to non treated cells). The hierarchical gene clustering was computed on median-gene-centered and log-transformed data using average linkage and uncentered correlation distances. Computations and visualization were performed using Cluster and TreeView software (Eisen et al., 1998). The Expression Analysis Systematic Explorer (EASE) and Gene Set analysis were used to determine the statistical over represented and differentially expressed genes (Tusher et al., 2001).
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| |
|
| Submission date |
Dec 21, 2010 |
| Last update date |
Dec 22, 2010 |
| Contact name |
frederique savagner |
| E-mail(s) |
[email protected]
|
| Phone |
+33241353314
|
| Fax |
+33241354017
|
| Organization name |
Inserm
|
| Department |
U694
|
| Street address |
4 rue larrey
|
| City |
angers |
| ZIP/Postal code |
49033 |
| Country |
France |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE26237 |
Effects of ionomycin (final concentration of 2 µM) and BAPTA/AM (final concentration of 6 µM) on the RO82 W-1 human thyroid cell line |
|
